Yes but only by creating a project using a selection from one directory and then adding images from other directories until all the elements of a project are in one place at any given time.
The issue is with "latent’ pending metadata changes that will only be found (allegedly) when you open that folder in DxPL and the updates occur “magically” or the ‘S’ icon shows that attention is needed.
I will try some tests later tonight or tomorrow and also re-read your post to make sure I understand it fully.